Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Brachyurin.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g1464 g1464.t21 TTS g1464.t21 11058577 11058577
chr_3 g1464 g1464.t21 isoform g1464.t21 11058703 11059664
chr_3 g1464 g1464.t21 exon g1464.t21.exon1 11058703 11058865
chr_3 g1464 g1464.t21 exon g1464.t21.exon2 11058988 11059274
chr_3 g1464 g1464.t21 cds g1464.t21.CDS1 11058988 11059274
chr_3 g1464 g1464.t21 exon g1464.t21.exon3 11059334 11059664
chr_3 g1464 g1464.t21 cds g1464.t21.CDS2 11059334 11059664
chr_3 g1464 g1464.t21 TSS g1464.t21 11059694 11059694

Sequences

>g1464.t21 Gene=g1464 Length=781
ATGAAGTTCTTTATTTTAATAGTTTCCTTATTTGCTGCAGTGTCAGCTTTTCCCAATAGA
GAAGAAAGGATCGTTGGTGGCTCAGTCGCTAAACCTAATTCGCATCCTTTTGTTGTACTT
CTTGTTGTCAATTTACCAAATCATAATGATGCAATGTGCGGAGGCTCAATAATCAGCAAA
ACAGTCATTTTAACTGCTGCACATTGCCTGCAAGGTTCAATTTCAACAGAAGTTGCAGCT
GGTGTTCACGACATCACACATGAAGAACCAACACAACAACATATGACTGTTATGCCTCCT
CAATATCGCGTTCATAGCCAATTCAATCCAAAAAATTTTAATAATGATGTGGCTACTTTA
ATTTTACCCCATCAATTGACTCTCAATAAGTATGTCGCAACAATAACATTGGCAAAAGCA
AATATAGGATTACTTGAAGGTGTAAATGCGATGTCGTTGGGTTGGGGAGACACAGTCAAT
GGTGGACCTCATTCGAATGTCTTAAAAGAGGTTACGAATAAAATTATCAAAAATTCTGAA
TGTGTTCCACATTATACAGGTGGAATTGTTAATGCTGCTGCTATGTGTGTTGCTTCGACC
AATAGAAATGGAATGTGATATTTTAATTTTAGGTCCTTTGGTAATTGCCCAAGGCAGCAA
TCTTATACAAGTTGGTATTGCAAGCTTCATTCCAACTCGTCCGAATACTTGTGGTGTAGT
TCCTGCTGGTTACGCTCGAGTCAGTTCTTTTATTGCATGGATTGAAAGTCATATGAAATA
A

>g1464.t21 Gene=g1464 Length=205
MKFFILIVSLFAAVSAFPNREERIVGGSVAKPNSHPFVVLLVVNLPNHNDAMCGGSIISK
TVILTAAHCLQGSISTEVAAGVHDITHEEPTQQHMTVMPPQYRVHSQFNPKNFNNDVATL
ILPHQLTLNKYVATITLAKANIGLLEGVNAMSLGWGDTVNGGPHSNVLKEVTNKIIKNSE
CVPHYTGGIVNAAAMCVASTNRNGM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1464.t21 CDD cd00190 Tryp_SPc 24 199 2.56718E-45
7 g1464.t21 Gene3D G3DSA:2.40.10.10 - 25 201 5.1E-40
6 g1464.t21 Gene3D G3DSA:2.40.10.10 - 36 134 5.1E-40
2 g1464.t21 PANTHER PTHR24260 - 3 202 4.4E-39
3 g1464.t21 PANTHER PTHR24260:SF90 AT07769P-RELATED 3 202 4.4E-39
1 g1464.t21 Pfam PF00089 Trypsin 24 199 8.7E-31
9 g1464.t21 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
10 g1464.t21 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
11 g1464.t21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
12 g1464.t21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
8 g1464.t21 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 205 -
14 g1464.t21 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 64 69 -
16 g1464.t21 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 24 205 17.503
15 g1464.t21 SMART SM00020 trypsin_2 23 204 6.3E-16
4 g1464.t21 SUPERFAMILY SSF50494 Trypsin-like serine proteases 6 201 4.27E-43
5 g1464.t21 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004252 serine-type endopeptidase activity MF
GO:0006508 proteolysis BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed